From 40d33aae8d7249422c61c7932ba41a10848def22 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 6 Mar 2024 09:37:55 +0100
Subject: [PATCH] fix minor bugs
---
src/bioflowinsighterror.py | 1 +
src/constant.py | 2 +-
src/operation.py | 7 ++++++-
src/outils.py | 16 ++++++++++++++++
src/process.py | 6 +++++-
src/workflow.py | 3 ++-
6 files changed, 31 insertions(+), 4 deletions(-)
diff --git a/src/bioflowinsighterror.py b/src/bioflowinsighterror.py
index d76b296..dd222bb 100644
--- a/src/bioflowinsighterror.py
+++ b/src/bioflowinsighterror.py
@@ -42,6 +42,7 @@ class BioFlowInsightError(Exception):
#* [3] -> unkonwn thing in a pipe operator
#* [5] -> A ternary conditional operator was used with an tuple
#* [7] -> Tuple with emit (ch1, ch2) = emit.out
+#* [9] -> Tuple with call (ch1, ch2) = wf()
diff --git a/src/constant.py b/src/constant.py
index 5c11ebc..a53afee 100644
--- a/src/constant.py
+++ b/src/constant.py
@@ -108,7 +108,7 @@ DOUBLE_DOT_TUPLE = r"\(\s*\w+\s*(,\s*\w+\s*)+\)\s*=\s*([^\?\n]+)\s*\?([^\n]+)"
END_OPERATOR = r' *(\(|{)'
ILLEGAL_CHARCTER_BEFORE_POTENTIAL_CHANNELS = r"\w|\'|\"|\."
ILLEGAL_CHARCTER_AFTER_POTENTIAL_CHANNELS = r"\w"
-MERGE_OPERATIONS = r'\.\s*((merge|mix|concat|spread|join|phase|cross|combine|fromList|collect|fromPath|value|from)\s*(\(|\{))'
+MERGE_OPERATIONS = r'\.\s*((merge|mix|concat|spread|join|phase|cross|combine|fromList|collect|fromPath|value|from|map)\s*(\(|\{))'#I've added map to this list cause channels can appear in map can concatenating channels -> it's a strange way of doing it
OPERATOR_IN_PIPE = r"\w+ *{[^}]*}|\w+ *\([^\)]*\)|\w+"
SET_OPERATORS = ["choice", "separate", "tap", "into", "set"]
TUPLE_EQUALS = r'\( *\w+( *, *\w+)+ *\) *=\s*(\w+)\s*\.'
diff --git a/src/operation.py b/src/operation.py
index b5e0da1..8f7b1e5 100644
--- a/src/operation.py
+++ b/src/operation.py
@@ -247,10 +247,15 @@ class Operation(Executor):
#================================
#Case channel1
#================================
- if(bool(re.fullmatch(constant.WORD, operation))):
+ if(bool(re.fullmatch(constant.WORD, operation.strip()))):
self.add_origin(operation)
+ #Case tupel with call -> this is not supported by BioFlow-Insight -> try calling first then using the emits
+ if(bool(re.fullmatch(r"\( *\w+ *(\, *\w+)+ *\) *= *Call_\d+", operation.strip()))):
+ raise BioFlowInsightError(f"A tuple is associated with an call{self.get_string_line(self.get_code(get_OG= True))}. BioFlow-Insight doesn't support this (see specification list), try defining the operation in a different way.", num=9, origin=self)
+
+
case_operation_starts_with_emit = False
#---------------------------
#Check emits
diff --git a/src/outils.py b/src/outils.py
index 8fa3780..a8082d4 100644
--- a/src/outils.py
+++ b/src/outils.py
@@ -683,6 +683,22 @@ def remove_jumps_inbetween_parentheses(code):
code = re.sub(r", *\n", ", ", code)
return code
+def remove_jumps_inbetween_curlies(code):
+ code = re.sub(',\s*\n\s*', ', ', code)
+ code = re.sub(';\s*\n\s*', '; ', code)
+ code = list(code)
+ curly_count = 0
+ for i in range(len(code)):
+ if(code[i]=="{"):
+ curly_count+=1
+ elif(code[i]=="}"):
+ curly_count-=1
+ elif(code[i]=="\n" and curly_count!=0):
+ code[i] = " "
+ code = "".join(code)
+ code = re.sub(r", *\n", ", ", code)
+ return code
+
#def check_if_parameter_is_given_pipe(code, OG_start, OG_end):
# char, end = get_next_element_caracter(code, OG_end-1)
# start = OG_end
diff --git a/src/process.py b/src/process.py
index ca7d81b..51acddc 100644
--- a/src/process.py
+++ b/src/process.py
@@ -2,7 +2,7 @@ import re
from .code_ import Code
from .nextflow_building_blocks import Nextflow_Building_Blocks
-from .outils import remove_jumps_inbetween_parentheses, sort_and_filter, get_dico_from_tab_from_id, check_if_element_in_tab_rocrate
+from .outils import remove_jumps_inbetween_parentheses, remove_jumps_inbetween_curlies, sort_and_filter, get_dico_from_tab_from_id, check_if_element_in_tab_rocrate
from .bioflowinsighterror import BioFlowInsightError
from . import constant
@@ -151,6 +151,7 @@ class Process(Nextflow_Building_Blocks):
def initialise_inputs_DSL1(self):
code = "\n"+self.get_input_code()+"\n"
code = remove_jumps_inbetween_parentheses(code)
+ code = remove_jumps_inbetween_curlies(code)
#Simplying the inputs -> when there is a jump line '.' -> it turns it to '.'
code = re.sub(constant.JUMP_DOT, '.', code)
@@ -191,6 +192,7 @@ class Process(Nextflow_Building_Blocks):
def initialise_inputs_DSL2(self):
code = self.get_input_code()
code = remove_jumps_inbetween_parentheses(code)
+ code = remove_jumps_inbetween_curlies(code)
for input in code.split("\n"):
input = input.strip()
if(input!=""):
@@ -208,6 +210,7 @@ class Process(Nextflow_Building_Blocks):
def initialise_outputs_DSL1(self):
code = self.get_output_code()
code = remove_jumps_inbetween_parentheses(code)
+ code = remove_jumps_inbetween_curlies(code)
def add_channel(name):
from .channel import Channel
output = Channel(name=name, origin=self.origin)
@@ -235,6 +238,7 @@ class Process(Nextflow_Building_Blocks):
def initialise_outputs_DSL2(self):
code = self.get_output_code()
code = remove_jumps_inbetween_parentheses(code)
+ code = remove_jumps_inbetween_curlies(code)
for output in code.split("\n"):
output = output.strip()
if(output!=""):
diff --git a/src/workflow.py b/src/workflow.py
index b29ea75..290a427 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -70,8 +70,9 @@ class Workflow:
with open(f'temp_dico_{id(self)}.json') as json_file:
self.dico = json.load(json_file)
os.system(f"rm temp_dico_{id(self)}.json")
+
except:
- None
+ _ = os.system(f"rm temp_dico_{id(self)}.json")
os.chdir(current_directory)
--
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